Input and runtime details for job 8257533 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 8257533 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:34:31 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:34:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:30:38 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:30:45 CET 2018
	Job Completed		@ Fri Feb 16 22:31:01 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=8257533&toolName=CopraRNA ( 30 days expiry )

Description of the job

LhrA2

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_003210 Listeria monocytogenes EGD-e

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
198	0.05669	0.7607	lmo2670	N/A	-16.54	0.050282	118 -- 190	141 -- 216		_____________117_________________191\n_____________\|___________________\|\n5'-AAU...AUUUG_________UACC______UUCAA...UCU-3'\n______________GAUGAGAUG____GGGAAC\n______________:\|\|\|\|\|\|\|\|____\|::\|\|\|\n______________UUACUCUAC____CUUUUG\n3'-GUU...GCCGG_________UUA_______UUUAU...GGA-5'\n_____________\|___________________\|\n_____________217_________________140\n	72 -- 78	165 -- 171	-16.0384 kcal/mol	2.83906 kcal/mol	0.941471 kcal/mol	117 191@LB@ \| \|@LB@5'-AAU...AUUUG UACC UUCAA...UCU-3'@LB@ GAUGAGAUG GGGAAC@LB@ :\|\|\|\|\|\|\|\| \|::\|\|\|@LB@ UUACUCUAC CUUUUG@LB@3'-GUU...GCCGG UUA UUUAU...GGA-5'@LB@ \| \|@LB@ 217 140@LB@@LB@@LB@Energy -16.54 kcal/mol@LB@Hybridization Energy -16.0384 kcal/mol@LB@Unfolding Energy - mRNA 2.83906 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 118 -- 190@LB@Position - sRNA 141 -- 216@LB@Position Seed - mRNA 72 -- 78@LB@Position Seed - sRNA 165 -- 171@LB@
199	0.05673	0.7607	lmo0888	N/A	-13.34	0.187096	200 -- 237	174 -- 211		_____________199___________________238\n_____________\|_____________________\|\n5'-AAG...GGCGG_____A__UAU__________ACGCA...AUA-3'\n______________AGUGA_GU___AAUGGAAGCA\n______________\|:\|\|\|_:\|___\|\|\|\|:\|\|:\|\|\n______________UUACU_UA___UUACUUUUGU\n3'-GUU...GCCGG_____C__C____________UUAUU...GGA-5'\n_____________\|_____________________\|\n_____________212___________________173\n	32 -- 38	155 -- 161	-11.9538 kcal/mol	2.24583 kcal/mol	0.954976 kcal/mol	199 238@LB@ \| \|@LB@5'-AAG...GGCGG A UAU ACGCA...AUA-3'@LB@ AGUGA GU AAUGGAAGCA@LB@ \|:\|\|\| :\| \|\|\|\|:\|\|:\|\|@LB@ UUACU UA UUACUUUUGU@LB@3'-GUU...GCCGG C C UUAUU...GGA-5'@LB@ \| \|@LB@ 212 173@LB@@LB@@LB@Energy -13.34 kcal/mol@LB@Hybridization Energy -11.9538 kcal/mol@LB@Unfolding Energy - mRNA 2.24583 kcal/mol@LB@Unfolding Energy - sRNA 0.954976 kcal/mol@LB@@LB@Position - mRNA 200 -- 237@LB@Position - sRNA 174 -- 211@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 155 -- 161@LB@
192	0.05535	0.7607	lmo2025	nadA	-15.59	0.075878	179 -- 223	172 -- 209	quinolinate synthetase	_____________178________________________________224\n_____________\|__________________________________\|\n5'-GAU...AAUAA_________U____UAGAA________ACA____ACAAU...CCC-3'\n______________AGGCAUGAA_UUAC_____ACGGUCGA___AGAU\n______________\|\|:\|\|\|\|\|\|_:\|\|\|_____\|\|\|\|:\|:\|___\|\|\|\|\n______________UCUGUACUU_GAUG_____UGCCGGUU___UCUA\n3'-GUU...CCGUA___________________________AC_____CUUAC...GGA-5'\n_____________\|__________________________________\|\n_____________210________________________________171\n	217 -- 223	172 -- 178	-24.6997 kcal/mol	5.14719 kcal/mol	11.5853 kcal/mol	178 224@LB@ \| \|@LB@5'-GAU...AAUAA U UAGAA ACA ACAAU...CCC-3'@LB@ AGGCAUGAA UUAC ACGGUCGA AGAU@LB@ \|\|:\|\|\|\|\|\| :\|\|\| \|\|\|\|:\|:\| \|\|\|\|@LB@ UCUGUACUU GAUG UGCCGGUU UCUA@LB@3'-GUU...CCGUA AC CUUAC...GGA-5'@LB@ \| \|@LB@ 210 171@LB@@LB@@LB@Energy -15.59 kcal/mol@LB@Hybridization Energy -24.6997 kcal/mol@LB@Unfolding Energy - mRNA 5.14719 kcal/mol@LB@Unfolding Energy - sRNA 11.5853 kcal/mol@LB@@LB@Position - mRNA 179 -- 223@LB@Position - sRNA 172 -- 209@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 172 -- 178@LB@
163	0.04467	0.7375	lmo1286	parE	-16.49	0.051436	172 -- 223	160 -- 211	DNA topoisomerase IV subunit B	_____________171____________________________224\n_____________\|______________________________\|\n5'-CUU...AAUCA______UAA__________AU_________UUUUA...UAC-3'\n______________GCUAGU___UGCUAUUCUG____AAGGUGG\n______________:\|\|\|\|\|___\|\|\|:\|\|\|\|\|:____\|\|\|:\|\|\|\n______________UGAUCA___ACGGUAAGAU____UUCUACC\n3'-GUU...CAGAC___________________AACC_______UAUGU...GGA-5'\n_____________\|______________________________\|\n_____________212____________________________159\n	135 -- 141	96 -- 102	-24.989 kcal/mol	7.49229 kcal/mol	9.10061 kcal/mol	171 224@LB@ \| \|@LB@5'-CUU...AAUCA UAA AU UUUUA...UAC-3'@LB@ GCUAGU UGCUAUUCUG AAGGUGG@LB@ :\|\|\|\|\| \|\|\|:\|\|\|\|\|: \|\|\|:\|\|\|@LB@ UGAUCA ACGGUAAGAU UUCUACC@LB@3'-GUU...CAGAC AACC UAUGU...GGA-5'@LB@ \| \|@LB@ 212 159@LB@@LB@@LB@Energy -16.49 kcal/mol@LB@Hybridization Energy -24.989 kcal/mol@LB@Unfolding Energy - mRNA 7.49229 kcal/mol@LB@Unfolding Energy - sRNA 9.10061 kcal/mol@LB@@LB@Position - mRNA 172 -- 223@LB@Position - sRNA 160 -- 211@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 96 -- 102@LB@
128	0.03459	0.6968	lmo1993	pdp	-15.44	0.080912	179 -- 212	139 -- 174	pyrimidine-nucleoside phosphorylase	_____________178_________________213\n_____________\|___________________\|\n5'-AUU...GAAAG____A___GA_________GGUGG...UUC-3'\n______________GGUG_AGA__AAUGAGAAU\n______________::\|\|_\|\|\|__\|\|\|\|\|:\|\|:\n______________UUAC_UCU__UUACUUUUG\n3'-GUU...GCCGG________AC_________UUUAU...GGA-5'\n_____________\|___________________\|\n_____________175_________________138\n	202 -- 208	156 -- 162	-13.005 kcal/mol	2.24337 kcal/mol	0.941471 kcal/mol	178 213@LB@ \| \|@LB@5'-AUU...GAAAG A GA GGUGG...UUC-3'@LB@ GGUG AGA AAUGAGAAU@LB@ ::\|\| \|\|\| \|\|\|\|\|:\|\|:@LB@ UUAC UCU UUACUUUUG@LB@3'-GUU...GCCGG AC UUUAU...GGA-5'@LB@ \| \|@LB@ 175 138@LB@@LB@@LB@Energy -15.44 kcal/mol@LB@Hybridization Energy -13.005 kcal/mol@LB@Unfolding Energy - mRNA 2.24337 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 179 -- 212@LB@Position - sRNA 139 -- 174@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 156 -- 162@LB@
149	0.0387	0.6968	lmo1809	plsX	-16.53	0.050633	188 -- 233	156 -- 203	glycerol-3-phosphate acyltransferase PlsX	_____________187________________234\n_____________\|__________________\|\n5'-ACA...CUGUA____C_____________CACGC...UUC-3'\n______________GAUG_GAUGGGUGGAGAU\n______________:\|\|\|_\|\|\|\|::\|\|:\|:\|:\n______________UUAC_CUACUUACUUUUG\n3'-GUU...GCCGG____U_____________UUUAU...GGA-5'\n_____________\|__________________\|\n_____________204________________155\n	227 -- 233	156 -- 162	-17.4325 kcal/mol	7.3364 kcal/mol	0.941471 kcal/mol	187 234@LB@ \| \|@LB@5'-ACA...CUGUA C CACGC...UUC-3'@LB@ GAUG GAUGGGUGGAGAU@LB@ :\|\|\| \|\|\|\|::\|\|:\|:\|:@LB@ UUAC CUACUUACUUUUG@LB@3'-GUU...GCCGG U UUUAU...GGA-5'@LB@ \| \|@LB@ 204 155@LB@@LB@@LB@Energy -16.53 kcal/mol@LB@Hybridization Energy -17.4325 kcal/mol@LB@Unfolding Energy - mRNA 7.3364 kcal/mol@LB@Unfolding Energy - sRNA 0.941471 kcal/mol@LB@@LB@Position - mRNA 188 -- 233@LB@Position - sRNA 156 -- 203@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 156 -- 162@LB@
82	0.02188	0.6733	lmo0200	prfA	-17.77	0.028863	191 -- 222	162 -- 204	listeriolysin positive regulatory protein	_____________190______223\n_____________\|________\|\n5'-UCA...AUUGG________ACAUG...AUC-3'\n______________GGGAUGAG\n______________\|\|\|\|\|\|\|\|\n______________CCCUACUC\n3'-GUU...UAUUG________CGUAU...GGA-5'\n_____________\|________\|\n_____________205______161\n	192 -- 198	197 -- 203	-14.1607 kcal/mol	1.90446 kcal/mol	0.386531 kcal/mol	190 223@LB@ \| \|@LB@5'-UCA...AUUGG ACAUG...AUC-3'@LB@ GGGAUGAG@LB@ \|\|\|\|\|\|\|\|@LB@ CCCUACUC@LB@3'-GUU...UAUUG CGUAU...GGA-5'@LB@ \| \|@LB@ 205 161@LB@@LB@@LB@Energy -17.77 kcal/mol@LB@Hybridization Energy -14.1607 kcal/mol@LB@Unfolding Energy - mRNA 1.90446 kcal/mol@LB@Unfolding Energy - sRNA 0.386531 kcal/mol@LB@@LB@Position - mRNA 191 -- 222@LB@Position - sRNA 162 -- 204@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 197 -- 203@LB@
138	0.03642	0.6968	lmo0509	prs	-15.18	0.090372	180 -- 241	157 -- 211	phosphoribosyl pyrophosphate synthetase	_____________179____________________________________242\n_____________\|______________________________________\|\n5'-AAC...GAAGA_____G______G__AG_____A_C_____C_______AUGAA...UCC-3'\n______________AAUUA_UAUGGC_GA__GAGAU_G_AAUGG_AGGCAAA\n______________\|\|:\|\|_:\|:\|\|\|_:\|__\|\|\|\|\|_\|_\|\|\|\|:_\|::\|\|\|\|\n______________UUGAU_GUGCCG_UU__CUCUA_C_UUACU_UUUGUUU\n3'-GUU...UGUAC____________G__A______________________AUUAC...GGA-5'\n_____________\|______________________________________\|\n_____________212____________________________________156\n	206 -- 212	153 -- 159	-24.2745 kcal/mol	6.00947 kcal/mol	10.6652 kcal/mol	179 242@LB@ \| \|@LB@5'-AAC...GAAGA G G AG A C C AUGAA...UCC-3'@LB@ AAUUA UAUGGC GA GAGAU G AAUGG AGGCAAA@LB@ \|\|:\|\| :\|:\|\|\| :\| \|\|\|\|\| \| \|\|\|\|: \|::\|\|\|\|@LB@ UUGAU GUGCCG UU CUCUA C UUACU UUUGUUU@LB@3'-GUU...UGUAC G A AUUAC...GGA-5'@LB@ \| \|@LB@ 212 156@LB@@LB@@LB@Energy -15.18 kcal/mol@LB@Hybridization Energy -24.2745 kcal/mol@LB@Unfolding Energy - mRNA 6.00947 kcal/mol@LB@Unfolding Energy - sRNA 10.6652 kcal/mol@LB@@LB@Position - mRNA 180 -- 241@LB@Position - sRNA 157 -- 211@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 153 -- 159@LB@
132	0.03532	0.6968	lmo1773	purB	-14.78	0.106383	9 -- 45	147 -- 186	adenylosuccinate lyase	_____________8___________________________46\n_____________\|___________________________\|\n5'-AUA...AUGUU____CU_____________________AUUAU...CUU-3'\n______________GAUG__GUGAAU__AAACAAAUGGUGA\n______________:\|\|\|__:\|\|\|\|\|__\|\|\|\|\|\|\|\|::\|\|\|\n______________UUAC__UACUUA__UUUGUUUAUUACU\n3'-GUU...GCCGG____UC______CU_____________AAAAC...GGA-5'\n_____________\|___________________________\|\n_____________187_________________________146\n	33 -- 39	153 -- 159	-18.9825 kcal/mol	5.01078 kcal/mol	5.96192 kcal/mol	8 46@LB@ \| \|@LB@5'-AUA...AUGUU CU AUUAU...CUU-3'@LB@ GAUG GUGAAU AAACAAAUGGUGA@LB@ :\|\|\| :\|\|\|\|\| \|\|\|\|\|\|\|\|::\|\|\|@LB@ UUAC UACUUA UUUGUUUAUUACU@LB@3'-GUU...GCCGG UC CU AAAAC...GGA-5'@LB@ \| \|@LB@ 187 146@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -18.9825 kcal/mol@LB@Unfolding Energy - mRNA 5.01078 kcal/mol@LB@Unfolding Energy - sRNA 5.96192 kcal/mol@LB@@LB@Position - mRNA 9 -- 45@LB@Position - sRNA 147 -- 186@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 153 -- 159@LB@
193	0.05586	0.7607	lmo1772	purC	-15.19	0.089756	256 -- 291	97 -- 135	phosphoribosylaminoimidazole-succinocarboxamide synthase	_____________255_____________________________________292\n_____________\|_______________________________________\|\n5'-UUA...AGAAG____________U__GU______UAUAA______C____CGACA...CGC-3'\n______________AAGCAGGUGUCU_GC__GUUGCU________GGA_GAUG\n______________\|\|:\|\|\|:\|\|\|\|\|_:\|__\|\|\|\|\|:________\|\|\|_\|\|\|\|\n______________UUUGUCUACAGA_UG__CAACGG________CCU_CUAC\n3'-GUU...ACAGA____________C__AU______UAAGAUAA___U____CUAUG...GGA-5'\n_____________\|_______________________________________\|\n_____________136_____________________________________96\n	261 -- 267	124 -- 130	-33.6761 kcal/mol	9.14329 kcal/mol	9.45249 kcal/mol	255 292@LB@ \| \|@LB@5'-UUA...AGAAG U GU UAUAA C CGACA...CGC-3'@LB@ AAGCAGGUGUCU GC GUUGCU GGA GAUG@LB@ \|\|:\|\|\|:\|\|\|\|\| :\| \|\|\|\|\|: \|\|\| \|\|\|\|@LB@ UUUGUCUACAGA UG CAACGG CCU CUAC@LB@3'-GUU...ACAGA C AU UAAGAUAA U CUAUG...GGA-5'@LB@ \| \|@LB@ 136 96@LB@@LB@@LB@Energy -15.19 kcal/mol@LB@Hybridization Energy -33.6761 kcal/mol@LB@Unfolding Energy - mRNA 9.14329 kcal/mol@LB@Unfolding Energy - sRNA 9.45249 kcal/mol@LB@@LB@Position - mRNA 256 -- 291@LB@Position - sRNA 97 -- 135@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 124 -- 130@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

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When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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